Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate GFF2033 PGA1_c20660 TRAP transporter, subunit DctM
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Phaeo:GFF2033 Length = 467 Score = 290 bits (742), Expect = 6e-83 Identities = 170/465 (36%), Positives = 268/465 (57%), Gaps = 44/465 (9%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGV-----NKFSL 55 M+ +L I L+LIG+P+A ALGLS+ + ++ I + + VA + F+L Sbjct: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTL---FLLIYSDSSLASVAGTLFEAFEGHFTL 57 Query: 56 LAIPFFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTA 115 LAIPFF+LA + M GG++RR++ F+ VG + GGL++ + A F A+SGSS A Sbjct: 58 LAIPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVV 117 Query: 116 SVGSVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAG 175 ++GS++I M + GY +EF+ V + +L PPS V+Y AA VS+ +F+AG Sbjct: 118 AIGSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVY--AAAVEVSVGRMFLAG 175 Query: 176 IMPGLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGV 235 ++PGL+ ++M + AK +N PKGE + E A A GL+ + IILGGI G+ Sbjct: 176 VIPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGI 235 Query: 236 FTATESAAVAVVWSFFVTMFIYRDY-------KWRD-------LPKLMHRTV-------- 273 FT TE+AAVA V++FFV F+YRD K +D LPK++ +TV Sbjct: 236 FTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFF 295 Query: 274 ------------RTISIVMILIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCIN 321 + ++ +I A +V+T Q+P +I TA L+ + L+ +N Sbjct: 296 HADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVN 355 Query: 322 FMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFV 381 +L++ G M+ + L++I+ P++ P+ +G+DP+H G+IM+VN+ IG+ITPPVG LFV Sbjct: 356 VILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFV 415 Query: 382 GSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLPSVVL 426 S + + + + V+A +PF LF+ L+ +TYIP IS LP+ V+ Sbjct: 416 TSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVM 460 Lambda K H 0.329 0.142 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 618 Number of extensions: 25 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 467 Length adjustment: 32 Effective length of query: 394 Effective length of database: 435 Effective search space: 171390 Effective search space used: 171390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory